††slugcomment: Draft version Seriola lalandi comprises three genetically distinct clades, with S. lalandi lalandi inhabiting the Southern Hemisphere. While a chromosome-level genome exists for the Northwestern Pacific S. lalandi aureovittata, no such resource is available for S. lalandi lalandi, limiting genetic research and aquaculture advancements. This study presents a high-quality chromosome-level genome assembly of S. lalandi lalandi using Illumina short-read, long-read (ONT) and Hi-C. A total of 289.12 Gb of raw genomic data was generated, and a final assembly of 644 Mb was produced with 99.64% of the assembled bases anchored into 24 pseudo-chromosomes. Genome annotation identified 24,600 protein-coding genes, with 96.1% completeness based on 3,640 BUSCO orthologs. Additionally, the complete mitogenome was assembled and annotated for S. lalandi lalandi. This genomic resource will help to inform comparative genomic studies, improve aquaculture breeding programs, and support appropriate fishery strategies, particularly in Aotearoa New Zealand, where S. lalandi lalandi is a culturally significant taonga species for M¯aori.

Seriola lalandi comprises three genetically distinct clades, with S. lalandi lalandi inhabiting the Southern Hemisphere. While a chromosome-level genome exists for the Northwestern Pacific S. lalandi aureovittata, no such resource is available for S. lalandi lalandi, limiting genetic research and aquaculture advancements. This study presents a high-quality chromosome-level genome assembly of S. lalandi lalandi using Illumina short-read, long-read (ONT) and Hi-C. A total of 289.12 Gb of raw genomic data was generated, and a final assembly of 644 Mb was produced with 99.64% of the assembled bases anchored into 24 pseudo-chromosomes. Genome annotation identified 24,600 protein-coding genes, with 96.1% completeness based on 3,640 BUSCO orthologs. Additionally, the complete mitogenome was assembled and annotated for S. lalandi lalandi. This genomic resource will help to inform comparative genomic studies, improve aquaculture breeding programs, and support appropriate fishery strategies, particularly in Aotearoa New Zealand, where S. lalandi lalandi is a culturally significant taonga species for M¯aori.

The identification of genetically distinct populations is central to the management and conservation of wild populations. Whole-genome-sequencing allows for high-resolution assessment of genetic structure, demographic connectivity and the impacts of selection acting on different parts of the genome. Here, we utilise population genomics to investigate the genetic structure of the Australasian snapper or Tāmure (Chrysophrys auratus), an ecologically, economically, and culturally important (taonga) marine fish. We analysed over four million high-quality SNPs obtained by whole-genome sequencing from 382 individuals collected across its New Zealand range. We identified two genetic clusters (an eastern and western cluster) with genetic disjunctions around on either side of the North Island of New Zealand. These genetic clusters do not match the current fisheries management areas. Pairwise-FST and ADMIXTURE analyses showed the presence of directional gene flow occurring at both genetic disjunctions from the East to the West cluster. We hypothesize that major ocean currents are limiting the dispersal of snapper at these genetic disjunctions. The heterogeneous coastal environment is also likely driving evolutionary change. A genome scan identified four significantly divergent genomic regions between genetic clusters. A diverse pattern of genetic variation in these regions implies that different evolutionary processes drive local adaptation in these clusters. Identification of candidate genes in these regions also provides a tentative connection to which traits may be under selection. Our results provide novel insights into New Zealand’s coastal environment influences evolutionary processes, and valuable information for effective management of the snapper fisheries.

Accelerated climate change is forcing species to adapt at unprecedented rates, but molecular mechanisms of how wild marine species adapt remain unclear. Here we use the marine teleost Chrysophrys auratus (Australasian snapper) as an exemplar high gene flow species to evaluate its ability to adapt to environmental pressures. Despite its commercial and cultural value in New Zealand, no detailed genomic analyses of its population structure have been performed. Using whole-genome sequencing of 382 individuals across 13 locations covering the New Zealand species range, we uncovered two distinct genetic clusters, a northeastern (NE-cluster) and a southwestern (SW-cluster) group, separated by distinct genetic discontinuities around Tauroa and Mahia Peninsulas. PCA, FST and admixture analyses clearly supported this split, revealing strong ancestry shifts at these geographic breaks, and areas around the genetic discontinuities where mixing of individuals from both clusters is occurring. Despite this high gene flow, we found compelling evidence of local adaptation in 38 significantly differentiated genomic regions. Two regions showed strong signs of a recent or ongoing selective sweep, each containing candidate genes linked to growth rate. For both regions, the NE-cluster exhibited directional selection, while the environmentally heterogeneous SW-cluster showed signatures of balancing selection. These patterns highlight the nuanced interplay between population connectivity, selection, and local environments and highlights the need to monitor both standing and adaptive genetic variation. As climate change accelerates, managing adaptive variation in marine teleosts like snapper will be critical to maintaining their resilience and sustainability under intensifying environmental pressures.

1) The more demanding requirements of DNA preservation for genomic research can be difficult to meet when field conditions limit the methodological approaches that can be used, or cause samples to be stored in suboptimal conditions. Such limitations may increase rates of DNA degradation, potentially rendering samples unusable for applications such as genome-wide sequencing. Nonetheless, little is known about the impact of suboptimal sampling conditions. 2) We evaluated the performance of two widely used preservation solutions (1. DESS: 20% DMSO, 0.25M EDTA, NaCl saturated solution, and 2. ethanol) under a range of storage conditions over a three-month period (sampling at 1 day, 1 week, 2 weeks, 1 month, and 3 months) to provide practical guidelines for DNA preservation. DNA degradation was quantified as the reduction in average DNA fragment size over time (DNA fragmentation) because the size distribution of DNA segments plays a key role in generating genomic datasets. Tissues were collected from a marine teleost species, the Australasian snapper, Chrysophrys auratus. 3) We found that the storage solution has a dramatic effect on DNA preservation. In DESS, DNA was only moderately degraded after three months of storage while DNA stored in ethanol showed high levels of DNA degradation already within 24 hours, making samples unsuitable for next-generation-sequencing. 4) We recommend DESS as the most promising solution to improve DNA preservation. These results provide practical and economical advice to improve DNA preservation when sampling for genome-wide applications. Keywords: DMSO, DNA preservation, ethanol, fish, next-generation-sequencing, NGS, snapper